After conceding two late goals, Bayern were denied an equaliser scored by Mathijs de Ligt.
Muller later fumed: "The referee did not go to VAR. He didn't even give himself a chance to go see it. Such a situation is very strange, whistling so fast.
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"It is an incredible decision. Normally, they let us run three metres until they finally blow the whistle. I don't know what happened."
Muller then referred to the defeat in 2017, a day in which Cristiano Ronaldo scored two controversial goals for Real Madrid.
"Sadly, this happens very often in Madrid," Muller added. "It happened to me in 2017 with two goals from Cristiano Ronaldo ... But it was before VAR."